number_clusters {multiClust} | R Documentation

## Function to determine the number of clusters to be used to cluster gene probes and samples.

### Description

Function to determine the number of clusters to be used to cluster gene probes and samples.

### Usage

    number_clusters(data.exp, Fixed = 3, gap_statistic = NULL)

### Arguments

`data.exp` | The numeric original gene expression matrix to be used for clustering of genes and samples. This object is an output of the input_file function.
`Fixed` | A positive integer used to represent the number of clusters the samples and probes will be divided into. The default cluster number is set to 3 clusters.
`gap_statistic` | A logical indicating whether to use the gap_statistic to determine the optimal number of clusters to divide samples into.

### Value

An object with the determined number of clusters to use.

### Note

The user should only choose either the fixed or gap_statistic option, not both. When using the gap_statistic option, change the argument to TRUE and "Fixed" to NULL.

### Author(s)

Nathan Lawlor, Alec Fabbri

### See Also

`clusGap`, `probe_ranking`

### Examples

    #Example 1: Using a fixed cluster number
    # Load in a test file
    data_file <- system.file("extdata", "GSE2034.normalized.expression.txt",
    package="multiClust")
    data <- input_file(data_file)
    clust_num <- number_clusters(data.exp=data, Fixed=3, gap_statistic=NULL)

    ## Not run:
    # Example 2: Using the gap_statistic to determine the optimal cluster number
    # Computation time is somewhat long
    clust_num <- number_clusters(data.exp=data, Fixed=NULL, gap_statistic=TRUE)

    ## End(Not run)

[Package multiClust version 1.12.0 Index]